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Hi all
I would like to merge my last branch(miguelrojasch-charges) to trunk:
The charges branches was created principally to solved some of the bugs
produced for some of the descriptors calculating partial charges based
on Gasteiger idea.
The new features are:
-﻿Added inchis ID in javaDoc.
-Check the result according tests
-Solved bug given different results calculating PartialPiCharges
depending how was started to be created the molecule object. Added Test.
-Solved bug given null results in some descriptor calculation. At least
know returns 0 value.
-solved bugs in the ConjugatedPiSystemsDetector method given errors by
reading.
-put all the descriptors with the corresponding extension module. e.g.
qsar.atomic with AtomicDescriptorTest and not molecular
-applying the concept that one descriptor must not depend on other
descriptors according the bug 186097. Applied for classes
{PartialTChargePEOEDescritpor, SigmaElectronegativity﻿Descritpor,
BondPartialPiCharge﻿Descritpor, BondPartialSigma﻿Descritpor,
BondPartialTCharge﻿Descritpor, BondSigmaElelctronegativty﻿Descritpor}.
[Still remaining the problem in IP descriptors]
Following the steps of the previous email I have obtained the given
results.
﻿The file diff.trunk.branch contains the difference between the
reports/*.txt files of trunk and branch with a plus o menus for each
line.
﻿with the command diff we can see an overview about what hat changed.
$ diff -u trunk.results branch.results | grep "^-Testcase" | wc -l
32
$ diff -u trunk.results branch.results | grep "^+Testcase" | wc -l
2
which are:
+Testcase:
testList(org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReaderTest)
+Testcase:
testIPDescriptor_5(org.openscience.cdk.qsar.descriptors.atomic.IPAtomicDescriptorTest)
the general overview is in trunk.branch.overview files. Using the script
from tools/﻿extractTestStats.bsh
The other comparing is between both repositories:
﻿svn diff http://cdk.svn.sourceforge.net/svnroot/cdk/cdk/trunkhttps://cdk.svn.sourceforge.net/svnroot/cdk/cdk/branches/miguelrojasch-CMLReact > diff.repo.trunk.branch
Best regards,
Miquel

On Tue, 2008-05-06 at 16:55 +0200, Egon Willighagen wrote:
> > -applying the concept that one descriptor must not depend on other
> > descriptors according the bug 186097. Applied for classes
> > {PartialTChargePEOEDescritpor, SigmaElectronegativity﻿Descritpor,
> > BondPartialPiCharge﻿Descritpor, BondPartialSigma﻿Descritpor,
> > BondPartialTCharge﻿Descritpor, BondSigmaElelctronegativty﻿Descritpor}.
> > [Still remaining the problem in IP descriptors]
>
> So, algorithms are now properly separate from QSAR descriptor wrapping?
Yes in fact. But only those which are correlated to charge and
electronegativity. I didn't check all descriptors.

﻿On Tue, 2008-05-06 at 16:55 +0200, Egon Willighagen wrote:
>
> I will browse through the patch... meanwhile, please send to this list
> which files are changed with your patch...
> You could do this by something like:
>
> $ grep Index <your-svn-diff-patch>
>
> as each line in that 'svn diff' patch with Index has a file name of a
> changed file...
>
Here is comming the results:
Regards,
Miquel

Miguel,
On Tue, May 6, 2008 at 4:55 PM, Egon Willighagen
<egon.willighagen@...> wrote:
> I will browse through the patch...
== 1 ==
- MDLReader reader = new MDLReader(ins, Mode.STRICT);
+ MDLReader reader = new MDLReader(ins);
Best to use Mode.STRICT... I guess the file is really a MDLV2000
file... in which case you should use MDLV2000Reader.
== 2 ==
+ * @cdk.inchi ?
+ *
Better no @cdk.inchi than a '?' ...
== 3 ==
I note some 10 commented out bit of code in
PartialPiChargeDescriptorTest.java:, marked with
/*TODO:REACT: revision*/
which needs to be addressed... (at least file a bug report about it...)
== 4 ==
-// logger.debug("WE : "+WE+" =
Dq("+Dq+")+fE("+fE+")*SumQN("+SumQN);
+ if(printResults)System.out.println("WE
: "+WE+" = Dq("+Dq+")+fE("+fE+")*SumQN("+SumQN);
Better restore to have it use the logger again
== 5 ==
Please use @cdk.keyword to annotate classes, so that people can find
your algorithms in the topic index [0].
== 6 ==
The patch currently consists some patches to remove code added to
trunk/, after you synched. So please make sure to make the patch
against the trunk/ version you last synched with.
Egon
0.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/keywords.html
--
----
http://chem-bla-ics.blogspot.com/

> == 3 ==
>
> I note some 10 commented out bit of code in
> PartialPiChargeDescriptorTest.java:, marked with
>
> /*TODO:REACT: revision*/
>
> which needs to be addressed... (at least file a bug report about it...)
>
The problem with the results from Gasteiger is that I am not complete
sure that his result make always sense.
That is the origen I put revision TODO. We should compare with other
software!
The rest indications I have already committed.
Miquel

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